ExcludonFinder: mapping transcriptional overlaps between neighboring genes.

ABSTRACT: Bacteria regulate neighboring genes via overlapping transcription in untranslated regions (UTRs), forming excludons. This overlap leads to transcriptional interference and RNase III-mediated mRNA degradation, resulting in mutually exclusive gene expression, where the activation of one gene suppresses its neighbor. Although individual examples of excludons have been described in various bacterial species, a comprehensive excludon map of a bacterial genome has yet to be established. In this study, we constructed the excludon map of Escherichia coli and Staphylococcus aureus using publicly available RNA-seq data and a newly developed computational tool, ExcludonFinder (https://excludonfinder-unavarra.com). Our analysis identified 16 divergent and 165 convergent excludons in E. coli, as well a

SUBMITTER: Sanmartin A 

PROVIDER: S-EPMC12288877 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature